X supports multi desktops and multi monitors for quite a long time now.
Usually you DO want to have your mouse and keyboard on all screens, so I think by default X will allow mouse and keyboard on all screens.
BUT - you can control which input devices (i.e mouse and keyboard) will work on which screen by manipulating the correct section in xorg.conf.
You should read about setting multiple displays with Xinerama, and about X.org.
Some time ago I had to deal with multiple displays, and while searching on google I stumbled on an HOWTO that explains how to have multiple X sessions for multiple users on one machine, and there they have to add a mouse and keyboard per session, so that could be a good place for you to start... if I find it again, I'll post it.
But look for 'Xinerama multiple screens' on google...





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